Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules

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Abstract

Ribosomal RNA (rRNA) molecules form highly conserved secondary and tertiary
structures via rRNA-rRNA and rRNA-protein interactions that collectively comprise the
macromolecule that is the ribosome. Because of their cellular universality, rRNA
molecules are commonly used for phylogeny estimations spanning all divergences of
life. In this dissertation, I elucidate the structure of several rRNAs by analyzing multiply
aligned sequences for basepair covariation and conserved higher order structural motifs.
Specifically, I predict novel structures for expansion segments D2 and D3 of the nuclear
large subunit rRNA (28S) and variable regions V4-V9 of the nuclear small subunit
rRNA (18S) from from 249 galerucine leaf beetles (Coleoptera: Chrysomelidae). I
describe a novel means for characterizing regions of alignment ambiguity that improves
methods for retaining phylogenetic information without violating nucleotide positional
homology. In the program PHASE, I explore a variety of RNA maximum likelihood
models using the 28S rRNA dataset and discuss the utitilty of these models in light of
their performance under Bayesian analysis. I conclude that seven-state models are likely
the best models to use for phylogenetic estimation, although I cannot determine with confidence which of the two seven-state models (7A or 7D) is better. Evaluation of the
unpaired sites within both rRNAs in Modeltest provided a similar model of evolution for
these non-pairing regions (TrN+ I+G). In addition, a sequenced region of the
mitochondrial cytochrome oxidase I gene (COI) from the galerucines was evaluated in
Modeltest, with each codon position modeled separately (GTR+I+G for positions 1 and
2, GTR+G for position 3). The combined galerucine dataset (28S+18S rRNA helices,
28S+18S rRNA unpaired sites, COI 1st, 2nd and 3rd positions) provided for two mixedmodel
Bayesian analysis of five discretely-modeled partitions (using 7A and 7D). The
results of these analyses are compared with those obtained from equally weighted
parsimony to provide a robust phylogenetic estimate of the Galerucinae and related leaf
beetle taxa. Finally, the odd characteristics of strepsipteran 18S rRNA are evaluated
through comparison of 12 strepsipterans with 163 structurally-aligned arthropod
sequences. Among other interesting results, I identify errors in previously published
strepsipteran sequences and predict structures not previously known from metazoan
rRNA.